Dockerfile

FROM ubuntu


RUN     apt-get update
RUN     apt-get install -y curl wget g++ make python libboost-dev libboost-thread-dev libboost-system-dev zlib1g-dev ncurses-dev unzip gzip bzip2 libxml2-dev libxslt-dev python-dev python-pip
WORKDIR /opt

RUN		mkdir /opt/bin

#install samtools
RUN     wget http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2
RUN     tar xvjf samtools-0.1.19.tar.bz2
RUN     cd /opt/samtools-0.1.19 && make
RUN     cp /opt/samtools-0.1.19/*.a /usr/local/lib/
RUN     mkdir /usr/local/include/bam
RUN     cp /opt/samtools-0.1.19/*.h /usr/local/include/bam/
RUN		cp /opt/samtools-0.1.19/samtools /opt/bin/

#install bowtie
RUN		wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.3/bowtie2-2.2.3-source.zip
RUN		unzip bowtie2-2.2.3-source.zip
RUN		cd /opt/bowtie2-2.2.3 && make && cp bowtie2* /opt/bin/

#install tophat
RUN     curl -O http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.12.tar.gz
RUN     tar xvzf tophat-2.0.12.tar.gz
RUN     cd /opt/tophat-2.0.12 && ./configure --prefix=/opt --with-boost-libdir=/usr/lib/x86_64-linux-gnu/ && make && make install

#install STAR
RUN     wget https://github.com/alexdobin/STAR/archive/STAR_2.4.0i.tar.gz
RUN     tar xvzf STAR_2.4.0i.tar.gz
RUN     cp /opt/STAR-STAR_2.4.0i/bin/Linux_x86_64/STAR /opt/bin/

#install python packages
RUN     pip install lxml


ENV		PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin